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(-) Description

Title :  CRYSTAL STRUCTURE OF C-TYPE LECTIN DOMAIN OF MURINE DENDRITIC CELL INHIBITORY RECEPTOR 2 IN COMPLEX WITH N-GLYCAN
 
Authors :  M. Nagae, K. Yamanaka, S. Hanashima, A. Ikeda, T. Satoh, N. Matsumoto, K. Yamamoto, Y. Yamaguchi
Date :  26 Sep 12  (Deposition) - 02 Oct 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  C-Type Lectin Fold, Cell Surface, Carbohydrate Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nagae, K. Yamanaka, S. Hanashima, A. Ikeda, K. Morita-Matsumoto, T. Satoh, N. Matsumoto, K. Yamamoto, Y. Yamaguchi
Recognition Of Bisecting N-Acetylglucosamine: Structural Basis For Asymmetric Interaction With The Mouse Lectin Dendritic Cell Inhibitory Receptor 2
J. Biol. Chem. V. 288 33598 2013
PubMed-ID: 24108122  |  Reference-DOI: 10.1074/JBC.M113.513572

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 4, MEMBER A4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD VECTOR
    Expression System Strain: ROSETTA DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 107-233
    Gene: DCIR2
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DENDRITIC CELL IMMUNORECEPTOR-2, DENDRITIC CELL INHIBITORY RECEPTOR 2, MCG1050915, PROTEIN CLEC4A4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MAN2Ligand/IonALPHA-D-MANNOSE
4MMA1Ligand/IonO1-METHYL-MANNOSE
5NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:196 , ASN A:198 , GLU A:202 , ASN A:217 , ASP A:218 , MAN A:1002BINDING SITE FOR RESIDUE CA A 1007
2AC2SOFTWAREVAL A:115 , SER A:148 , GLN A:149 , ALA A:150 , ARG A:203 , LYS A:222 , HOH A:1148 , HOH A:1149BINDING SITE FOR RESIDUE SO4 A 1008
3AC3SOFTWARESER A:106 , PRO A:113 , GLY A:213 , TRP A:214 , HOH A:1127 , HOH A:1178 , HOH A:1179BINDING SITE FOR RESIDUE SO4 A 1009
4AC4SOFTWAREMAN A:1004 , NAG A:1005 , NAG A:1006BINDING SITE FOR RESIDUE EDO A 1010
5AC5SOFTWARETHR A:183 , GLU A:196 , ASN A:198 , TRP A:201 , GLU A:202 , ASN A:208 , ASN A:217 , ASP A:218 , ILE A:219 , PRO A:220 , ASP A:223 , HIS A:225 , LYS A:232 , CA A:1007 , EDO A:1010 , HOH A:1130 , HOH A:1131 , HOH A:1134 , HOH A:1136 , HOH A:1155 , HOH A:1156 , HOH A:1166 , HOH A:1167BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1001 TO 1006

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:118
2A:136 -A:229
3A:204 -A:221

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:196 -Pro A:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VYK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VYK)

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000793791ENSMUSE00000520646chr6:122940385-12294046682Q5YIR8_MOUSE1-28280--
1.2ENSMUST000000793792ENSMUSE00000463896chr6:122941778-122941894117Q5YIR8_MOUSE28-67400--
1.3ENSMUST000000793793ENSMUSE00000464662chr6:122954027-122954128102Q5YIR8_MOUSE67-101350--
1.4ENSMUST000000793794ENSMUSE00000552557chr6:122962721-122962875155Q5YIR8_MOUSE101-152521A:106-15247
1.5ENSMUST000000793795ENSMUSE00000552554chr6:122963777-122963889113Q5YIR8_MOUSE153-190381A:153-19038
1.6ENSMUST000000793796ENSMUSE00000504342chr6:122973917-122974123207Q5YIR8_MOUSE190-236471A:190-23344

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:128
 aligned with Q5YIR8_MOUSE | Q5YIR8 from UniProtKB/TrEMBL  Length:236

    Alignment length:128
                                   115       125       135       145       155       165       175       185       195       205       215       225        
         Q5YIR8_MOUSE   106 CCPKDWKPFVSHCYFILNDSKASWNESEEKCSHMGAHLVVIHSQAEQDFITSNLNTSAGYFIGLLDAGQRQWRWIDQTPYNKSATFWHKGEPNQDWERCVIINHKTTGWGWNDIPCKDEHNSVCQVKK 233
               SCOP domains d3vyka_ A: automated matches                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhh......eeeeeee.....eee........................eeeeeee..eeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:106-152 UniProt: 101-152      Exon 1.5  PDB: A:153-190              ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.6  PDB: A:190-233 UniProt: 190-236    Transcript 1 (2)
                 3vyk A 106 SCPKDWKPFVSHCYFILNDSKASWNESEEKCSHMGAHLVVIHSQAEQDFITSNLNTSAGYFIGLLDAGQRQWRWIDQTPYNKSATFWHKGEPNQDWERCVIINHKTTGWGWNDIPCKDEHNSVCQVKK 233
                                   115       125       135       145       155       165       175       185       195       205       215       225
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VYK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VYK)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5YIR8_MOUSE | Q5YIR8)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0097367    carbohydrate derivative binding    Interacting selectively and non-covalently with a carbohydrate derivative.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5YIR8_MOUSE | Q5YIR8: 3vyj

(-) Related Entries Specified in the PDB File

3vyj